This is way too late, and Ken's already pretty much addressed it, but I
thought I might as well chime in.

Clearly the inventory of codepoints in Unicode is intended to be emic,
so the diversity of glyph variants of antiquity are not proper to it.
Where some typographical tradition does make a consistent
differentiation between two glyphs, though, they are candidates for
separate codepoints.

While normal sigma and lunate sigma are indeed mere glyph variants in
most contexts --- the lunate being early mediaeval, and not much seen
in modern typography --- there is a context where it is used routinely:
editions of old texts where the editor is being deliberately agnostic
about whether the sigma is final or not. Often, the editor merely
carries that through as a stylistic choice to the rest of the text; but
given that in antiquity text was written without spaces, there is a
semantic loading to the choice of non-final and final sigma which the
lunate obviates. (e.g. if you're publishing a papyrus, you often put on
facing pages what the papyrus actually has --- with lunates, since the
papyrus give no indication of word breaks, so it would be presumptuous
to put in medials and finals --- and what you think it says --- again
with lunates, so that the two facing pages look consistent, if nothing
else.) So the lunate sigma is distinct in modern practice and necessary.

The lunate capital becomes necessary for completeness and consistency
(all-caps rendering of ancient texts, say). It might be possible to
insist that those editors using lunate capital in title case are merely
using an affectation, and that lunate should be the same codepoint as
the capital normal sigma. But I think that makes matters much more
complicated than they need be.

As I describe on http://www.opoudjis.net/dist/sigma.html , while there
are cases in typographical traditions where the form of sigma used is
not predictable (medial word-finally, final word-medially), they are
almost all deviant and rare enough that they can be ignored. So in most
cases, even the medial/final distinction is unnecessary (just as the
medial/final beta distinction would be --- if anyone still observed
it...) The one exception is abbreviation, because period is
semantically overloaded.

This is not to say that all that has been included in Unicode has been
included well; Haralambous in his '99 paper doubts that mathematicians
could use upsilon-hook or cursive kappa with semantic differentiation
from their normal forms, and I doubt it too. But that's clearly a
legacy issue now, and nothing much can be done about it, even if the
variants end up not being used distinctly by mathematicians.

The story with the koppa is that the lightning-bolt koppa is used in
Modern Greek as a numeral not only in legislation, but pretty much
anywhere English would use a Roman numeral -- notably in page numbering
of introductions, and enumeration of points. So the context one would
likeliest find both numeric and q-like koppa would be a Modern Greek
scholarly work on Archaic Greek inscriptions. Not extremely frequent,
but it can happen. And it is true that most Greeks would have no idea
that the lightning-bolt koppa is the same character as the q-like
koppa, since outside of at most a mumbled sentence in the Classical
stream at high school, most will have never seen a q-like koppa at all.